Home-plate umpire Mark Ripperger initially ruled Ellsbury safe on the sacrifice-fly attempt to right by Dustin Pedroia, as he looked at Bard lying flat on his back with no ball in his glove.
But Bard held on to the ball in his bare hand throughout the collision after clearly tagging Ellsbury before he slid home.
Mariners manager Eric Wedge and pitcher Felix Hernandez raced to home plate and were arguing with Ripperger over the fallen Bard, who still clutched the ball in his hand.
Once the umpires huddled and reversed the call, Francona grew heated and ultimately was tossed. It was Francona's fourth ejection of the year and 33rd of his career.
Bard credited the umpires for making the right call in the end.
"I get what he saw," Bard said. "When the throw came in, like I always do I tried to put the ball in my bare hand and then tag with two hands. He looked at my glove and the ball was in my bare hand.
"I think everybody could see the guy was out. Obviously, it was a big run. But credit goes to Ich. He made a great throw and gave me a good, long hop to work with. We're just glad to get out of there with a win."
Ellsbury didn't argue with the decision in the end.
"It looked like he held on to the ball, made the tag and then pulled out with his bare hand to show that he got me," the Red Sox leadoff man said. "From my angle it looked like he got the call right. Both players were going hard. He knows he's going to get hit pretty hard going for the tag and I knew I was trying to break it up.
"It's one of those calls that's easy to overturn if the other umpires can tell if he held on to the ball."
Francona said he just wanted to know what was going on.
"I just didn't understand why the home-plate umpire didn't explain it to me," he said. "It was his call. They are so protective of the young guys. They have the ability to make a call and then don't explain it to me. They knew I was going to get thrown out. Sometimes that's the way it goes.
"It's very unusual for them to reverse. Whatever. I told them I was going to get thrown out before he was done with the explanation. That's just what happens. Move on."